Yousef Nadarkhani has now been charged with "acting against national security", Zionist activities and evangelism, and he has until Sunday to fund a £25,000 bail or face detention.
The accusation regarding national security is "a common charge" brought against church leaders in Iran, according to the Christian anti-persecution charity Middle East Concern.
Mr Nadarkhani was sentenced to death in June 2011 - with a provision for annulment if he renounced his Christian faith - after being charged with apostasy and evangelism in September the previous year.
He was arrested in October 2009 after he claimed the Iranian government's policy of enforcing Qur'an lessons in schools contradicted the constitutional freedom to practice religion.
After an international outcry, the death sentence was dropped in September 2012, following a retrial which led to Mr Nadarkhani's acquittal.
Yousef and his wife were arrested in May 2016 - along with three other people who have since been released after they each paid £25,000 bail.
In a statement, Middle East Concern said: "Those close to Pastor Yousef Nadarkhani request prayer that the oppressive actions against Yousef will stop and the new charges of 'acting against national security' will be dropped..
"..[That] God will give His peace to Yousef and his family, and [that] they will not be anxious and all officials involved will love mercy, act justly, learn about Jesus and choose to follow Him."